Digital Commons Network^™

The Function Of Field Study: Comparison Of Limited And Full Field Experience Courses, Lauren Fine, Telyn Peterson, Mat Duerden, Riley Nelson, John Bennion

Faculty Publications

Fieldwork, an experiential and outdoor component of a traditional lecture class, has been effective in improving students’ content knowledge and attitudes. However, most studies of these courses use a full lecture course as the comparison group rather than comparing amounts or types of fieldwork. This study compares two classes that incorporate fieldwork (n = 18 and 12 participants, respectively) and uses both quantitative and qualitative methods to analyze changes in content knowledge, self-efficacy, and perceived value of the subject (entomology). Pre-and post-test scores suggest that information memorization is best taught in a traditional classroom environment. Qualitative data illustrate that the …

Fluoroscopic System For Assessment Of In Vivo Hindfoot Kinematics During Gait: Control Data And Applications In Osteogenesis Imperfecta, Ben Mchenry, Jason Long, Peter Smith, Haluk Altiok, Gerald F. Harris

Biomedical Engineering Faculty Research and Publications

No abstract provided.

Walker Design For Kinetic Assessment Of Upper Extremity Joint Demands In Children With Osteogenesis Imperfecta, Katherine A. Konop, Kelly M.B. Strifling, Mei Wang, Jeffrey P. Schwab, Jeffrey D. Ackman, Peter A. Smith, Gerald F. Harris

Biomedical Engineering Faculty Research and Publications

No abstract provided.

Influence Of Neural Network Training Parameters On Short-Term Wind Forecasting, Adel Brka, Yasir M. Al-Abdeli, Ganesh Kothapalli

Research outputs 2014 to 2021

This paper investigates factors which can affect the accuracy of short-term wind speed prediction when done over long periods spanning different seasons. Two types of neural networks (NNs) are used to forecast power generated via specific horizontal axis wind turbines. Meteorological data used are for a specific Western Australian location. Results reveal that seasonal variations affect the prediction accuracy of the wind resource, but the magnitude of this influence strongly depends on the details of the NN deployed. Factors investigated include the span of the time series needed to initially train the networks, the temporal resolution of these data, the …

Should We Sync? Seascape-Level Genetic And Ecological Factors Determine Seagrass Flowering Patterns, Marlene Jahnke, Jordi F. Pagès, Teresa Alcoverro, Paul S. Lavery, Kathryn M. Mcmahon, Gabriele Procaccini

Research Datasets

Spatial and temporal heterogeneity in flowering occur in many plant species with abiotic pollination and may confer fitness advantages through mechanisms such as predator satiation or pollination efficiency. Environmental factors such as light quality or quantity and temperature play an important role in inducing synchronisation on wide geographic scales. On a smaller geographic scale, external factors such as resource availability and herbivory are theorised to trigger flowering, while genetic factors may also play an important role. In this study, we assessed the importance of ecological and genetic factors in shaping seascape-level spatial heterogeneity in flowering of the seagrass Posidonia oceanica. …

Rcd+: Fast Loop Modeling Server, José R. López-Blanco, Alejandro J. Canosa-Valis, Yaohang Li, Pablo Chacón

Computer Science Faculty Publications

Modeling loops is a critical and challenging step in protein modeling and prediction. We have developed a quick online service (http://rcd.chaconlab.org) for ab initio loop modeling combining a coarse-grained conformational search with a full-atom refinement. Our original Random Coordinate Descent (RCD) loop closure algorithm has been greatly improved to enrich the sampling distribution towards near-native conformations. These improvements include a new workflow optimization, MPI-parallelization and fast backbone angle sampling based on neighbor-dependent Ramachandran probability distributions. The server starts by efficiently searching the vast conformational space from only the loop sequence information and the environment atomic coordinates. The generated closed loop …

Flexc: Protein Flexibility Prediction Using Context-Based Statistics, Predicted Structural Features, And Sequence Information, Ashraf Yaseen, Mais Nijim, Brandon Williams, Lei Qian, Min Li, Jianxin Wang, Yaohang Li

Computer Science Faculty Publications

The fluctuation of atoms around their average positions in protein structures provides important information regarding protein dynamics. This flexibility of protein structures is associated with various biological processes. Predicting flexibility of residues from protein sequences is significant for analyzing the dynamic properties of proteins which will be helpful in predicting their functions.

Deep Models For Brain Em Image Segmentation: Novel Insights And Improved Performance, Ahmed Fakhry, Hanchuan Peng, Shuiwang Ji

Computer Science Faculty Publications

Motivation: Accurate segmentation of brain electron microscopy (EM) images is a critical step in dense circuit reconstruction. Although deep neural networks (DNNs) have been widely used in a number of applications in computer vision, most of these models that proved to be effective on image classification tasks cannot be applied directly to EM image segmentation, due to the different objectives of these tasks. As a result, it is desirable to develop an optimized architecture that uses the full power of DNNs and tailored specifically for EM image segmentation.

Results: In this work, we proposed a novel design of DNNs for …

Examining The Potential Clinical Value Of Curcumin In The Prevention And Diagnosis Of Alzheimer's Disease, K. G. Goozee, T. M. Shah, Hamid R. Sohrabi, Stephanie Rainey-Smith, B. Brown, Guiseppe Verdile, Ralph Martins

Research outputs 2014 to 2021

Curcumin derived from turmeric is well documented for its anti-carcinogenic, antioxidant and anti-inflammatory properties. Recent studies show that curcumin also possesses neuroprotective and cognitive-enhancing properties that may help delay or prevent neurodegenerative diseases, including Alzheimer’s disease (AD). Currently, clinical diagnosis of AD is onerous, and it is primarily based on the exclusion of other causes of dementia. In addition, phase III clinical trials of potential treatments have mostly failed, leaving disease-modifying interventions elusive. AD can be characterised neuropathologically by the deposition of extracellular β amyloid (Aβ) plaques and intracellular accumulation of tau-containing neurofibrillary tangles. Disruptions in Aβ metabolism/clearance contribute to …

Comparing Biological Markers Of Alzheimer's Disease Across Blood Fraction And Platforms: Comparing Apples To Oranges, Sid E. O'Bryant, Simone Lista, Robert A. Rissman, Melissa Edwards, Fan Zhang, James Hall, Herik Zetterberg, Simon Lovestone, Veer Bular Gupta, Neill Graff-Radford, Ralph N. Martins, Andreas Jeromin, Stephen Waring, Esther Oh, Mitchel Kling, Laura D. Baker, Harald Hampel

Research outputs 2014 to 2021

Introduction:

This study investigated the comparability of potential Alzheimer's disease (AD) biomarkers across blood fractions and assay platforms.

Methods:

Nonfasting serum and plasma samples from 300 participants (150 AD patients and 150 controls) were analyzed. Proteomic markers were obtained via electrochemiluminescence or Luminex technology. Comparisons were conducted via Pearson correlations. The relative importance of proteins within an AD diagnostic profile was examined using random forest importance plots.

Results:

On the Meso Scale Discovery multiplex platform, 10 of the 21 markers shared > 50% of the variance across blood fractions (serum amyloid A R2 = 0.99, interleukin (IL)10 R2 = 0.95, fatty …

Genetic Model, Feifei Zhao, Manshu Song, Youxin Wang, Wei Wang

Research outputs 2014 to 2021

No abstract provided.

Linking Vital Rates Of Landbirds On A Tropical Island To Rainfall And Vegetation Greenness, James F. Saracco, Paul Radley, Peter Pyle, Erin Rowan, Ron Taylor, Lauren Helton

Research outputs 2014 to 2021

Remote tropical oceanic islands are of high conservation priority, and they are exemplified by range-restricted species with small global populations. Spatial and temporal patterns in rainfall and plant productivity may be important in driving dynamics of these species. Yet, little is known about environmental influences on population dynamics for most islands and species. Here we leveraged avian capture-recapture, rainfall, and remote-sensed habitat data (enhanced vegetation index [EVI]) to assess relationships between rainfall, vegetation greenness, and demographic rates (productivity, adult apparent survival) of three native bird species on Saipan, Northern Mariana Islands: rufous fantail (Rhipidura rufifrons), bridled white-eye (Zosterops conspicillatus), and …

Individual And Population-Level Responses To Ocean Acidification, Ben P. Harvey, Niall J. Mckeown, Samuel P. Rastrick, Camilla Bertolini, Andy Foggo, Helen Graham, Jason M. Hall-Spencer, Marco Milazzo, Paul W. Shaw, Daniel P. Small, Philippa J. Moore

Research outputs 2014 to 2021

Ocean acidification is predicted to have detrimental effects on many marine organisms and ecological processes. Despite growing evidence for direct impacts on specific species, few studies have simultaneously considered the effects of ocean acidification on individuals (e.g. consequences for energy budgets and resource partitioning) and population level demographic processes. Here we show that ocean acidification increases energetic demands on gastropods resulting in altered energy allocation, i.e. reduced shell size but increased body mass. When scaled up to the population level, long-term exposure to ocean acidification altered population demography, with evidence of a reduction in the proportion of females in the …

Stick Or Switch: A Selection Heuristic Predicts When People Take The Perspective Of Others Or Communicate Egocentrically, Shane Rogers, Nicholas Fay

Research outputs 2014 to 2021

This paper examines a cognitive mechanism that drives perspective-taking and egocentrism in interpersonal communication. Using a conceptual referential communication task, in which participants describe a range of abstract geometric shapes, Experiment 1 shows that perspective-taking and egocentric communication are frequent communication strategies. Experiment 2 tests a selection heuristic account of perspective-taking and egocentric communication. It uses participants' shape description ratings to predict their communication strategy. Participants' communication strategy was predicted by how informative they perceived the different shape descriptions to be. When participants' personal shape description was perceived to be more informative than their addressee's shape description, there was a …

Profiling Igg N-Glycans As Potential Biomarker Of Chronological And Biological Ages: A Community-Based Study In A Han Chinese Population, Xinwei Yu, Youix Wang, Jasminka Krištić, Jing Dong, Xi Chu, Siqi Ge, Hao Wang, Honghong Fang, Qing Gao, Di Lui, Zhongya Zhao, Hongli Peng, Maja P. Baković, Lijuan Wu, Manshu Song, Igor Rudan, Harry Campbell, Gordan Lauc, Wei Wang

Research outputs 2014 to 2021

As an important post-translation modifying process, glycosylation significantly affects the structure and function of immunoglobulin G (IgG) molecules and is essential in many steps of the inflammatory cascade. Studies have demonstrated the potential of using glycosylation features of IgG as a component of predictive biomarkers for chronological age in several European populations, whereas no study has been reported in Chinese. Herein, we report various patterns of changes in IgG glycosylation associated with age by analyzing IgG glycosylation in 701 community-based Han Chinese (244 males, 457 females; 23-68 years old). Eleven IgG glycans, including FA2B, A2G1, FA2[6]G1, FA2[3]G1, FA2[6]BG1, FA2[3]BG1, A2G2, …

Incorporating Field Studies Into Species Distribution And Climate Change Modelling: A Case Study Of The Koomal Trichosurus Vulpecula Hypoleucus (Phalangeridae), Shaun Molloy, Robert Davis, Eddie Van Etten

Research outputs 2014 to 2021

Species distribution models (SDMs) are an effective way of predicting the potential distribution of species and their response to environmental change. Most SDMs apply presence data to a relatively generic set of predictive variables such as climate. However, this weakens the modelling process by overlooking the responses to more cryptic predictive variables. In this paper we demonstrate a means by which data gathered from an intensive animal trapping study can be used to enhance SDMs by combining field data with bioclimatic modelling techniques to determine the future potential distribution for the koomal (Trichosurus vulpecula hypoleucus). The koomal is a geographically …

Floating Constructed Wetland For The Treatment Of Polluted River Water: A Pilot Scale Study On Seasonal Variation And Shock Load, Tanveer Saeed, Biprojit Paul, Rumana Afrin,, Abdullah Al-Muyeed, Guangzhi Sun

Research outputs 2014 to 2021

This paper reports the performance of a pilot scale floating constructed wetland (FCW), employed for the treatment of polluted water collected from Buriganga river in Bangladesh. The FCW system included a tank for accommodating collected water and a floating mat with media, to support the growth of two macrophyte species Phragmites australis and Canna indica. Mean mass removal rates of 0.66, 0.76, 0.08, 0.51, 2.49g/m2d were achieved for ammoniacal nitrogen (NH4-N), total inorganic nitrogen (TIN), phosphorus (P), biochemical oxygen demand (BOD), chemical oxygen demand (COD), respectively by the FCW. Nitrogen removal was via nitrification-denitrification processes, whereas filtration-sedimentation appeared to influence …

Regular Fat And Reduced Fat Dairy Products Show Similar Associations With Markers Of Adolescent Cardiometabolic Health, Theresa A. O'Sullivan, Alexandra P. Bremmer, Trevor A. Mori, Lawrence J. Beilin, Charlotte Wilson, Katherine Hafekost, Gina L. Ambrosini, Rae Chi Huang, Wendy H. Oddy

Research outputs 2014 to 2021

Reduced fat dairy products are generally recommended for adults and children over the age of two years. However, emerging evidence suggests that dairy fat may not have detrimental health effects. We aimed to investigate prospective associations between consumption of regular versus reduced fat dairy products and cardiometabolic risk factors from early to late adolescence. In the West Australian Raine Study, dairy intake was assessed using semi-quantitative food frequency questionnaires in 860 adolescents at 14 and 17-year follow-ups; 582 of these also had blood biochemistry at both points. Using generalized estimating equations, we examined associations with cardiometabolic risk factors. Models incorporated …

Seagrass Sediments Reveal The Long-Term Deterioration Of An Estuarine Ecosystem, Oscar Serrano, Paul S. Lavery, Pere Masque, Karina Inostroza, James Bongiovanni, Carlos Duarte

Research Datasets

The database compiles published data (in Serrano et al. 2016, Global Change Biology, doi:10.1111/gcb.13195) on temporal trends in biogeochemical variables in the Posidonia australis sediment core from Oyster Harbour, Western Australia. The core studied encompasses the last 500 years of history. Data on dry bulk density, carbonate content, sedimentso.

Greater Strength Gains After Training With Accentuated Eccentric Than Traditional Isoinertial Loads In Already Strength-Trained Men, Simon Walker, Anthony J. Blazevich, Greg Haff, James J. Tufano, Robert Newton, Keijo Häkkinen

Research outputs 2014 to 2021

As training experience increases it becomes more challenging to induce further neuromuscular adaptation. Consequently, strength trainers seek alternative training methods in order to further increase strength and muscle mass. One method is to utilize accentuated eccentric loading, which applies a greater external load during the eccentric phase of the lift as compared to the concentric phase. Based upon this practice, the purpose of this study was to determine the effects of 10 weeks of accentuated eccentric loading vs. traditional isoinertial resistance training in strength-trained men. Young (22 ± 3 years, 177 ± 6 cm, 76 ± 10 kg, n = …

Aβ-Related Memory Decline In Apoe Ε4 Noncarriers: Implications For Alzheimer Disease, Yen Ying Lim, Simon Laws, Victor Villemagne, Robert Pietrzak, Tenielle Porter, David Ames, Christoher Fowler, Stephanie Rainey-Smith, Peter Snyder, Ralph Martins, Olivier Salvado, Pierrick Bourgeat, Christopher Rowe, Colin Masters, Paul Maruff

Research outputs 2014 to 2021

Objective:

As the absence of Aβ-related memory decline in APOE ϵ4 noncarriers may be due to the relative brevity of previous studies, we aimed to characterize Aβ-related cognitive decline over 72 months in APOE ϵ4 carriers and noncarriers who were cognitively normal (CN).

Methods:

CN older adults (n 423) underwent Aβ imaging and APOE genotyping. Participants completed comprehensive neuropsychological testing at baseline 18-, 36-, 54-, and 72-month assessments.

Results:

Relative to Aβ- CN ϵ4 noncarriers, both Aβ+ CN ϵ4 carriers and noncarriers showed significantly increased decline in measures of memory, language, and executive function as well as higher rates of …

A Review Of Current Neuromorphic Approaches For Vision, Auditory, And Olfactory Sensors, Anup Vanarse, Adam Osseiran, Alexander Rassau

Research outputs 2014 to 2021

Conventional vision, auditory, and olfactory sensors generate large volumes of redundant data and as a result tend to consume excessive power. To address these shortcomings, neuromorphic sensors have been developed. These sensors mimic the neuro-biological architecture of sensory organs using aVLSI (analog Very Large Scale Integration) and generate asynchronous spiking output that represents sensing information in ways that are similar to neural signals. This allows for much lower power consumption due to an ability to extract useful sensory information from sparse captured data. The foundation for research in neuromorphic sensors was laid more than two decades ago, but recent developments …

1h-Nmr Urinary Metabolomic Profiling For Diagnosis Of Gastric Cancer, Angela W. Chan, Pascal Mercier, Daniel Schiller, Robert Bailey, Sarah Robbins, Dean T. Eurich, Michael B. Sawyer, David Broadhurst

Research outputs 2014 to 2021

Background:

Metabolomics has shown promise in gastric cancer (GC) detection. This research sought to identify whether GC has a unique urinary metabolomic profile compared with benign gastric disease (BN) and healthy (HE) patients.

Methods:

Urine from 43 GC, 40 BN, and 40 matched HE patients was analysed using ¹H nuclear magnetic resonance (¹H-NMR) spectroscopy, generating 77 reproducible metabolites (QC-RSD < 25%). Univariate and multivariate (MVA) statistics were employed. A parsimonious biomarker profile of GC vs HE was investigated using LASSO regularised logistic regression (LASSO-LR). Model performance was assessed using Receiver Operating Characteristic (ROC) curves.

Results:

GC displayed a clear discriminatory biomarker profile; the BN profile overlapped with GC and HE. LASSO-LR identified …

Autoantibody Production In Cancer—The Humoral Immune Response Toward Autologous Antigens In Cancer Patients, Pauline Zaenker, Elin Solomonovna Gray, Melanie Ruth Ziman

Research outputs 2014 to 2021

A link between autoimmune responses and cancer via autoantibodies was first described in the 1950s. Since, autoantibodies have been studied for their potential use as cancer biomarkers, however the exact causes of their production remain to be elucidated. This review summarizes current theories of the causes of autoantibody production in cancer, namely:

1) defects in tolerance and inflammation,

2) changes in protein expression levels,

3) altered protein structure, and

4) cellular death mechanisms.

We also highlight the need for further research into this field to improve our understanding of autoantibodies as biomarkers for cancer development and progression.

Association Between Igf2bp2 Polymorphisms And Type 2 Diabetes Mellitus: A Case-Control Study And Meta-Analysis, Ping Rao, Hao Wang, Honghong Fang, Qing Gao, Jie Zhang, Manshu Song, Yong Zhou, Youxin Wang, Wei Wang

Research outputs 2014 to 2021

Background:

Genome-wide association studies (GWAS) found that IGF2BP2 rs4402960 and rs1470579 polymorphisms were associated with type 2 diabetes mellitus (T2DM) risk. Many studies have replicated this association, but yielded inconsistent results.

Materials and Methods:

A case-control study consisting of 461 T2DM patients and 434 health controls was conducted to detect the genetic susceptibility of IGF2BP2 in a northern Han Chinese population. A meta-analysis was to evaluate the association more precisely in Asians.

Results:

In the case-control study, the carriers of TT genotype at rs4402960 had a higher T2DM risk than the G carriers (TG + GG) (adjusted …

Consistent Prebiotic Effect On Gut Microbiota With Altered Fodmap Intake In Patients With Crohn's Disease: A Randomised, Controlled Cross-Over Trial Of Well-Defined Diets, Emma P. Halmos, Claus T. Christophersen, Anthony R. Bird, Susan J. Shepherd, Jane G. Muir, Peter R. Gibson

Research outputs 2014 to 2021

OBJECTIVES:

Altering FODMAP (fermentable oligosaccharides, disaccharides, monosaccharides and polyols) intake has substantial effects on gut microbiota. This study aimed to investigate effects of altering FODMAP intake on markers of colonic health in patients with Crohn’s disease.

METHODS:

After evaluation of their habitual diet, 9 patients with clinically quiescent Crohn’s disease were randomised to 21 days of provided low or typical (“Australian”) FODMAP diets with ≥ 21-day washout in between. Five-day fecal samples were collected at the end of each diet and analyzed for calprotectin, pH, short-chain fatty acids (SCFA) and bacterial abundance. Gastrointestinal symptoms were recorded daily.

RESULTS:

Eight participants …

Developmental Transcription Factors In Age-Related Cns Disease: A Phoenix Rising From The Ashes?, Robert White, Meghan Thomas

Research outputs 2014 to 2021

Few would doubt that understanding the developmental landscape from which a mature neuron is derived is essential to understand its biology. The temporal and spatial position of a cell from the very earliest stages of development predicts the unique combinations of growth factors it will subsequently be exposed to. This combination of factors determines the transcriptional platform set within the cell by its specific combination of transcription factors, who direct the show. This, in turn, determines what cell type it will differentiate into, and what connections it will make. How this developmental platform translates to maintenance of a differentiated neuron …

Finding Chemopreventatives To Reduce Amyloid Beta In Yeast, Ian Macreadie, Costa Arvanitis, Prashant Bharadwaj

Research outputs 2014 to 2021

Alzheimer's disease (AD) is the most common form of age-related dementia with the latest report (WorldAlzheimerReport, 2015) showing 46.8 million people are currently affected by dementia. That number is expected to double every 20 years unless there is effective therapeutic intervention.

The Competing Objectives Underlying The Protection Of Intangible Cultural Heritage, Peter K. Yu

Faculty Scholarship

One topic that has received considerable academic and policy attention concerns the key objectives underlying the establishment of this new framework. To help us develop a better and deeper understanding, this article outlines eight most widely documented objectives. While some of these objectives overlap or conflict with each other, others touch on issues that are of only marginal concern to some constituencies. By focusing on each objective in turn, this article aims to underscore the divergent, and at times competing, interests among the many stakeholders involved in the framework.

Although some readers may find the description of all eight underlying …

Diagnostics Of Primary Immunodeficiencies Through Next-Generation Sequencing., Vera Gallo, Laura Dotta, Giuliana Giardino, Emilia Cirillo, Vassilios Lougaris, Roberta D'Assante, Alberto Prandini, Rita Consolini, Emily G. Farrow, Isabelle Thiffault, Carol J. Saunders, Antonio Leonardi, Alessandro Plebani, Raffaele Badolato, Claudio Pignata

Manuscripts, Articles, Book Chapters and Other Papers

BACKGROUND: Recently, a growing number of novel genetic defects underlying primary immunodeficiencies (PIDs) have been identified, increasing the number of PID up to more than 250 well-defined forms. Next-generation sequencing (NGS) technologies and proper filtering strategies greatly contributed to this rapid evolution, providing the possibility to rapidly and simultaneously analyze large numbers of genes or the whole exome.

OBJECTIVE: To evaluate the role of targeted NGS and whole exome sequencing (WES) in the diagnosis of a case series, characterized by complex or atypical clinical features suggesting a PID, difficult to diagnose using the current diagnostic procedures.

METHODS: We retrospectively analyzed …